In-form Villa crashed out of the FA Cup at Goodison Park without the services of Heskey, who was replaced in O'Neill's starting XI by John Carew, who is himself still playing his way back from a long-term injury.
O'Neill was left fuming in midweek after England boss Fabio Capello started Heskey against Spain, despite the striker being not fully fit due to an Achilles problem.
Heskey's injury was exacerbated by his appearance in Seville and his club boss has reiterated his disappointment over the England management's decision to risk him in a friendly fixture.
He said: "Gareth Barry being suspended was our fault, our problem. Being without Heskey is not our fault.
"He should not have played on Wednesday for England because he had an existing Achilles injury and made it worse.
"He had come off against Blackburn with the same injury, and he arrived with England with the injury. Of course Heskey wants to play for England, like every other player.
Sent home"But Luke Young was unable to play with an injured toe. He showed his face at the England camp and was sent home.
"The same should have happened to Heskey, I would have had a better chance of him playing in the cup tie if that had happened.
"And now Curtis Davies has a shoulder injury, it came out of place. With some manipulation it was put back and he wanted to continue to play.
"But I believe it is something that has happened before and we must have a good look at this problem now."
O'Neill concedes both Heskey and Davies are now doubts for Wednesday's Uefa Cup game against CSKA Moscow.
"I really don't know whether Heskey or Davies will be fit for the Uefa Cup tie on Wednesday against CSKA Moscow."